NCBI Antimicrobial Resistance Gene Finder Plus (AMRFinderPlus)

Overview for AMRFinderPlus 4.0

This software and the accompanying database identify acquired antimicrobial resistance genes in bacterial protein and/or assembled nucleotide sequences as well as known resistance-associated point mutations for several taxa. With AMRFinderPlus we added select members of additional classes of genes such as virulence factors, biocide, heat, acid, and metal resistance genes.

Note that AMRFinderPlus reports gene and point mutation presence/absence; it does not infer phenotypic resistance. Many of the resistance genes detected by AMRFinderPlus may not be relevant for clinical management or antimicrobial surveillance. See the Note regarding Genotype vs. Phenotype for more information.

As of version 4.0 AMRFinderPlus includes StxTyper.

Run amrfinder -u to get the most recent release version of the database before using. See New in AMRFinderPlus and the list of releases for more information on what's new.

Installation

AMRFinder requires BLAST and HMMER. We provide instructions using BioConda to install the prerequisites.

Installation Instructions

Running AMRFinderPlus

Examples Usage (syntax/options) Tips and tricks

Methods

AMRFinder can be run in multiple modes with protein sequence as input and/or with DNA sequence as input. To get maximum information it should be run with both protein and nucleotide. When run with protein sequence it uses both BLASTP and HMMER to search protein sequences for AMR genes along with a hierarchical tree of gene families to classify and name novel sequences. With nucleotide sequences it uses BLASTX translated searches and the hierarchical tree of gene families. Adding the --organism option enables screening for point mutations in select organisms and suppresses the reporting of some that are extremely common in those organisms.

Running AMRFinderPlus Interpreting results Methods AMRFinderPlus database

A note about ABRicate

Many people use ABRicate with the default "ncbi" database. It has come to our attention that at least some of those users think they are getting the same results they would get from AMRFinderPlus and that NCBI recommends. ABRicate uses a subset of the AMRFinderPlus database and different methods to do AMR gene detection. While we love Torsten and ABRicate, the results are not the same as those you would get by running AMRFinderPlus. To identify AMR genes from assembled sequence we recommend using AMRFinderPlus to get the full value out of the NCBI compiled database, including correct gene symbols, named allele vs. novel allele determination, protein-based search/naming, curated cutoffs, HMM searches, etc.

Related Resources

• Pathogen Detection AMR resources and Help docs regarding those resources. The Pathogen Detection team at NCBI has a page describing the AMR Resources we provide and Help docs regarding those resources.
• Browse the AMRFinderPlus database on the web
  • Pathogen Detection Reference Gene Catalog - Proteins used by AMRFinderPlus in table form with query, filtering, and additional metadata. This information is also included in a tab-delimited file Reference Gene Catalog on FTP.
  • Pathogen Detection Reference Gene Hierarchy - The hierarchical organization of genes and HMMs used by our curators and AMRFinderPlus to allow accurate naming of genes.
  • Pathogen Detection Reference HMM Catalog - HMMs used by AMRFinderPlus in table form with query, filtering, and additional metadata
• Pathogen Detection Isolates Browser - NCBI runs AMRFinderPlus on all microbial genome assemblies in the Pathogen Detection system (over 1,500,000 isolate assemblies). Gene symbols from AMRFinderPlus runs, along with other metadata for the isolates are visible in the Isolates Browser
• MicroBIGG-E - Detailed AMRFinderPlus results for individual elements, links to sequence, and additional metadata are included in the Pathogen Detection Microbial Browser for Identification of Genetic and Genomic Elements (MicroBIGG-E)

amrfinder-announce mailing list

Subscribe to the amrfinder-announce mailing list to get updates when we release new versions of the software or database. This is a low-traffic list.

Help

If you have any questions about or experience problems running AMRFinderPlus, please contact [email protected].

See Version 1 documentation for the old AMRFinder version 1 software

License / Public Domain Notice

Publication

See our our AMRFinderPlus paper for more details.

How to cite

To make your methods repeatable you should state both the version of the software and the version of the database that you used in your work. For example: "We used AMRFinderPlus version 3.11.11 with database version 2023-04-17.1 to identify antimicrobial resistance genes and point mutations in the assemblies (Feldgarden et al. 2021)."

Citation

AMRFinderPlus

Feldgarden M, Brover V, Gonzalez-Escalona N, Frye JG, Haendiges J, Haft DH, Hoffmann M, Pettengill JB, Prasad AB, Tillman GE, Tyson GH, Klimke W. AMRFinderPlus and the Reference Gene Catalog facilitate examination of the genomic links among antimicrobial resistance, stress response, and virulence. Sci Rep. 2021 Jun 16;11(1):12728. doi: 10.1038/s41598-021-91456-0. PMID: 34135355; PMCID: PMC8208984.

AMRFinder

Feldgarden M, Brover V, Haft DH, Prasad AB, Slotta DJ, Tolstoy I, Tyson GH, Zhao S, Hsu CH, McDermott PF, Tadesse DA, Morales C, Simmons M, Tillman G, Wasilenko J, Folster JP, Klimke W. Validating the AMRFinder Tool and Resistance Gene Database by Using Antimicrobial Resistance Genotype-Phenotype Correlations in a Collection of Isolates. Antimicrob Agents Chemother. 2019 Oct 22;63(11):e00483-19. doi: 10.1128/AAC.00483-19. Erratum in: Antimicrob Agents Chemother. 2020 Mar 24;64(4): PMID: 31427293; PMCID: PMC6811410.